I'll describe what I see, and if you are getting a better outcome, I'd really like to hear.

I am currently able to play 720p MP4 content from a shared drive on my AppleTV. It works great, but means I have to transcode, and I lose Dolby Digital audio
I would like to be able to play 720p MKV files held on a shared network drive. These files are about a Gig for 45 mins. Which I reckon averages at 0.5 Megabytes per second.
That's easily within the speed of my network.

According to the Perian people - their forum and the to-do tickets in the project....
Perian needs to fully load the entire MKV file prior to playing. This is an acknowledged issue, and is scheduled to be improved in subsequent releases.

On a Mac Pro - with a 270mbs 802.11n network (which delivers 9megaBYTES per second) - VLC will play 720pMKV content flawlessly across the network.

But, if I use Quicktime/Perian 1.0 to load a 720p MKV file on a network drive, I see a loading bar in Quicktime. Perian has to pre-scan all MKV files.
For a 1GB file, it takes about 3-4 mins to load the file fully before playing. A wired gigabit ethernet link would be a bit faster.
If I press play *before* the loading completes, I get stuttering.
With the same file on a local drive, the loading is obviously faster (about a minute) and stuttering goes away if I press play early.

But on the AppleTV Perian's MKV implementation poses another problem.

The h264 module on the AppleTV only plays a subset of h264 content.
This means that only 50% of MKVs will play, the rest get a black screen.

Replacing the h264 component will result in that being fixed, but the replacement component is much less efficient on the Apple TV.
Not only is it not fast enough for 720p MKVs - it means that 720p MP4s will not play smoothly either.

So the choice is 50% of MKVs are black.
Or
No 720p content at all.

NitoTV uses Mplayer to play MKVs without Perian's pre-loading process.
However it drops a lot of frames, which would not be too bad, except that frame drops cause the audio and video to go out of sync.

MKV playback on the Apple TV is still a work-in-progress but certainly looks possible.
I'm keen to see this happen because I have lots of 720p MKV 24fps h264 content.

There are currently two solutions for the AppleTV.

Perian is an add-on for Quicktime. The unreleased-still-in-beta Perian 1.0 does allow MKV playback. However the way it works requires the entire file to be read into Quicktime before it plays smoothly. If you install the Perian beta onto a Mac, you'll see a loading progress bar at the bottom of the player. Obviously playing files over a wireless network is going to be pretty lousy with this solition.

However sometime after the release of 1.0, the Perian team intend to improve the way this works.
Because it's a Quicktime component, it will mean that MKV will work with the brilliant AppleTVFiles plugin.

Another plugin for the AppleTV is NitoTV. This is a port of MPlayer - and plays 720p MKVs quite well. This player drops the odd frame, and after a while the audio has drifted out of sync. Nito is not great yet - but it proves that the Apple TV certainly has enough power to play 720p content.